Development of Computational Methods for Proteomic Analysis As proteome projects come on line and produce data, the need for effective computational tools is paramount. The goal of this project is development of computational resources to address those needs. The focus of development in the first two years will be guided by the proteome analysis project now being undertaken in Dr. Ray Gesteland's laboratories at the University of Utah. The development of computational tools will proceed in stages to best address the needs of the project. Specifically, a basic data handling infrastructure and database system will be implemented first and will be designed with extensibility as a key goal. Second, existing mass spec and protein analysis software tools will be incorporated into the infrastructure for initial analysis work. The third step will then develop software which utilizes database information (sequence, annotations, cDNA's, mass spectra) as well as information from predictive tools (e.g. ORF determination) to identify proteins and their corresponding coding regions, and pinpoint proteins which may have arisen due to RNA coding events such as frameshift, codon redefinition (e.g. secis), and mRNA bypassing. The later stages of the project will then leverage this work to study expression data and intron sequence data (via comparative analysis) and their relation to the proteome.